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Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways.

ABSTRACT: We recently proposed a new bioinformatic algorithm called OncoFinder for quantifying the activation of intracellular signaling pathways. It was proved advantageous for minimizing errors of high-throughput gene expression analyses and showed strong potential for identifying new biomarkers. Here, for the first time, we applied OncoFinder for normal and cancerous tissues of the human bladder to identify biomarkers of bladder cancer. Using Illumina HT12v4 microarrays, we profiled gene expression in 17 cancer and seven non-cancerous bladder tissue samples. These experiments were done in two independent laboratories located in Russia and Canada. We calculated pathway activation strength values for the investigated transcriptomes and identified signaling pathways that were regulated differently in bladder cancer (BC) tissues compared with normal controls. We found, for both experimental datasets, 44 signaling pathways that serve as excellent new biomarkers of BC, supported by high area under the curve (AUC) values. We conclude that the OncoFinder approach is highly efficient in finding new biomarkers for cancer. These markers are mathematical functions involving multiple gene products, which distinguishes them from "traditional" expression biomarkers that only assess concentrations of single genes.

SUBMITTER: Lezhnina K

PROVIDER: S-EPMC4253415 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways.

Lezhnina Ksenia K Kovalchuk Olga O Zhavoronkov Alexander A AA Korzinkin Mikhail B MB Zabolotneva Anastasia A AA Shegay Peter V PV Sokov Dmitry G DG Gaifullin Nurshat M NM Rusakov Igor G IG Aliper Alexander M AM Roumiantsev Sergey A SA Alekseev Boris Y BY Borisov Nikolay M NM Buzdin Anton A AA

Oncotarget 20141001 19

We recently proposed a new bioinformatic algorithm called OncoFinder for quantifying the activation of intracellular signaling pathways. It was proved advantageous for minimizing errors of high-throughput gene expression analyses and showed strong potential for identifying new biomarkers. Here, for the first time, we applied OncoFinder for normal and cancerous tissues of the human bladder to identify biomarkers of bladder cancer. Using Illumina HT12v4 microarrays, we profiled gene expression in ...[more]

PMID: 25296972

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Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways.

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Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways.

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